Urea to Albumin Ratio Is an Excellent Predictor of Death in Patients With Complicated Intra-Abdominal Infections.

Background: The urea to albumin ratio (UAR) has shown a prognostic value in various clinical settings, however, no study has yet investigated its ability to predict outcome in complicated intra-abdominal infections (cIAIs). Therefore, our aim was to evaluate the association between UAR and mortality in such patients. Patients and Methods: A single-center prospective study including 62 patients with cIAIs was performed at a University Hospital Stara Zagora for the period November 2018 to August 2021. Various routine laboratory and clinical parameters were recorded before surgery and on post-operative day 3. We used serum levels of urea and albumin to calculate the UAR. Results: The observed in-hospital mortality was 14.5%. Non-survivors had higher pre- and post-operative median of UAR than survivors (88.39 vs. 30.99, p < 0.0001 and 106.18 vs. 26.58, p < 0.0001, respectively). Lethal outcome was predicted successfully both by UAR before surgery (area under receiver operating characteristics [AUROC] curves = 0.889; p < 0.0001) at a threshold of 61.42 and on third post-operative day (AUROC = 0.943; p < 0.0001) at a threshold = 55.89. Conclusions: Peri-operative UAR showed an excellent ability for prognostication of fatal outcome in patients with cIAIs.

Better chance of survival is associated with higher neutrophil CD16 expression in patients with complicated intra-abdominal infections.

Aim: The ability of neutrophil CD16 (nCD16) expression to predict outcome in complicated intra-abdominal infections (cIAIs) has not yet been studied; therefore we aimed to evaluate its potential prognostic value in such patients. Methods: Between November 2018 and August 2021 a single-center prospective study was performed in the Department of Surgical Diseases at a University Hospital Stara Zagora. A flow cytometry was used to measure the levels of nCD16 before surgery and on the 3rd postoperative day (POD) in 62 patients with cIAIs. Results: We observed a mortality rate of 14.5% during hospitalization. Survivors had significantly higher perioperative expression of nCD16 than non-survivors (P = 0.02 preoperatively and P = 0.006 postoperatively). As predictor of favorable outcome we found a good predictive performance of preoperative nCD16 (AUROC = 0.745) and a very good predictive performance of postoperative levels (AUROC = 0.846). An optimal preoperative threshold nCD16 = 34.75 MFI permitted prediction of survival with sensitivity and specificity of 66.7% and 77.8%, respectively. A better sensitivity of 72.5% and specificity of 85.7% were observed for threshold = 54.8 MFI on the 3rd POD. Conclusion: Perioperative neutrophil CD16 expression shows a great potential as a predictor of favorable outcome in patients with cIAIs.

Prediction of outcome using CD14++CD16-, CD14++CD16+ and CD14+CD16++ monocyte subpopulations in patients with complicated intra-abdominal infections.

There is still no study investigating the prognostic performance of CD14++CD16-, CD14++CD16+ and CD14+CD16++ monocyte subpopulations in complicated intra-abdominal infections (cIAIs); therefore, we aimed to evaluate the association between monocyte subtypes and outcome in such patients. A single-center prospective study was conducted at a University Hospital Stara Zagora between November 2018 and August 2021. Preoperatively and on the 3rd postoperative day (POD), we measured the levels of CD14++CD16-, CD14++CD16+ and CD14+CD16++ monocytes in peripheral blood using flow cytometry in 62 patients with cIAIs and 31 healthy controls. Nine of the 62 patients died during hospitalization. Survivors had higher pre-surgery percentages of CD14++CD16- classical monocytes and higher percentage of these cells predicted favorable outcome in ROC analysis (AUROC = 0.781, p = 0.008). The CD14++CD16+ intermediate monocyte percentages were higher in non-survivors both pre- and postoperatively but only the higher preoperative values predicted a lethal outcome (AUROC = 0.722, p = 0.035). For CD14+CD16++ non-classical monocytes, non-survivors had lower percentages on day 3 post-surgery and low percentage was predictive of lethal outcome (AUROC = 0.752, p = 0.046). Perioperative levels of monocyte subpopulations in peripheral blood show a great potential for prognostication of outcome in patients with cIAIs.

Prognostic performance of neutrophil CD64 expression in patients with complicated intra-abdominal infections - a prospective study.

No study yet analyzed the prognostic abilities of neutrophil CD64 expression (nCD64) in complicated intra-abdominal infections (cIAIs), therefore our aim was to evaluate the possible association between this biomarker and outcome in such patients. This single-center prospective study was conducted in the Department of Surgical Diseases at a University Hospital 'Prof. Dr. Stoyan Kirkovich' Stara Zagora for the period November 2018 - August 2021. We used flow cytometry to measure the percentage of nCD64 preoperatively and on the 3rd postoperative day (POD) in 62 patients with cIAIs and 31 healthy controls. Of the 62 enrolled patients, nine (14.5%) died during hospitalization. The perioperative expression of nCD64 was significantly higher in non-survivors compared to survivors (p = 0.02 before surgery and p = 0.024 after surgery). ROC Curve analysis revealed the good prognostic value of pre- and postoperative nCD64 levels as mortality predictors (AUROC = 0.744 and 0.765, respectively). Preoperatively, the identified sensitivity and specificity for nCD64 cut-off = 94.8% were 66.7% and 84.6%, respectively and on the 3rd POD for nCD64 cut-off = 84.85% we observed a sensitivity of 71.4% and a specificity of 78.8%. Neutrophil CD64 shows good prognostic value in patients with cIAIs both preoperatively and on the 3rd POD.

Can we predict death using scoring systems in patients with local peritonitis ? A retrospective study.

INTRODUCTION: Prognostic scores in patients with local peritonitis (LP) have not yet been studied exhaustively. AIM: We, therefore, aimed in this study to evaluate the ability of several scoring systems to predict death in LP. MATERIALS AND METHODS: A retrospective analysis including 68 patients with LP was conducted at Prof. Dr. Stoyan Kirkovich University Hospital in Stara Zagora from January 2017 to August 2021. Clinical and laboratory data needed for calculating the scoring systems were collected at admission or postoperatively. We compared the prognostic performance of WSES SSS, MPI, SIRS, and qSOFA using area under the receiver operation characteristics (AUROC) curves and bivariate correlation analysis. RESULTS: The observed mortality rate was 8.8%. Among all scores, MPI showed the best prognostic performance (AUROC=0.805, 95% CI 0.660-0.950). A threshold MPI >25 points permitted prediction of adverse outcome with a sensitivity of 66.7% and a specificity of 80.6%. The only significant correlation was found between outcome and MPI (p=0.012, r=0.302). Conclusions: The MPI has the ability to prognosticate mortality in patients with LP unlike WSES SSS, qSOFA and SIRS.

The Multiverse of Plant Small RNAs: How Can We Explore It?

Plant small RNAs (sRNAs) are a heterogeneous group of noncoding RNAs with a length of 20-24 nucleotides that are widely studied due to their importance as major regulators in various biological processes. sRNAs are divided into two main classes-microRNAs (miRNAs) and small interfering RNAs (siRNAs)-which differ in their biogenesis and functional pathways. Their identification and enrichment with new structural variants would not be possible without the use of various high-throughput sequencing (NGS) techniques, allowing for the detection of the total population of sRNAs in plants. Classifying sRNAs and predicting their functional role based on such high-performance datasets is a nontrivial bioinformatics task, as plants can generate millions of sRNAs from a variety of biosynthetic pathways. Over the years, many computing tools have been developed to meet this challenge. Here, we review more than 35 tools developed specifically for plant sRNAs over the past few years and explore some of their basic algorithms for performing tasks related to predicting, identifying, categorizing, and quantifying individual sRNAs in plant samples, as well as visualizing the results of these analyzes. We believe that this review will be practical for biologists who want to analyze their plant sRNA datasets but are overwhelmed by the number of tools available, thus answering the basic question of how to choose the right one for a particular study.

Analysis of the complete mitochondrial genome sequence of the resurrection plant Haberlea rhodopensis.

Haberlea rhodopensis is a paleolithic tertiary relict species that belongs to the unique group of resurrection plants sharing remarkable tolerance to desiccation. When exposed to severe drought stress, this species shows an ability to maintain structural integrity of its deactivated photosynthetic apparatus, which easily reactivates upon rehydration. In addition to its homoiochlorophyllous nature, the resurrection capability of H. rhodopensis is of particular importance to the global climate change mitigation. In this study, we sequenced, assembled, and analyzed the mitochondrial (mt) genome of H. rhodopensis for the first time. The master circle has a typical circular structure of 484 138 bp in length with a 44.1% GC content in total. The mt genome of H. rhodopensis contains 59 genes in total, including 35 protein-coding, 21 tRNAs, and 3 rRNAs genes. 7 tandem repeats and 85 simple sequence repeats (SSRs) are distributed throughout the mt genome. The alignment of 20 plant mt genomes confirms the phylogenetic position of H. rhodopensis in the Lamiales order. Our comprehensive analysis of the complete mt genome of H. rhodopensis is a significant addition to the limited database of organelle genomes of resurrection species. Comparative and phylogenetic analysis provides valuable information for a better understanding of mitochondrial molecular evolution in plants.

Prognostic value of peripheral blood CD14+HLA-DR+ monocytes in patients with acute pancreatitis.

Acute pancreatitis (AP) is characterized by a potent pro-inflammatory response and concomitant anti-inflammatory response leading to a state of immunosuppression. Decreased HLA (Human Leukocyte Antigen)-DR expression on monocytes is a reliable cellular marker of immune suppression. The main objective of this study was to investigate the clinical value of the percentage of peripheral blood CD14+ HLA-DR+ monocytes (mHLA-DR) for diagnosis and assessment of severity, development of organ failures (OF), local complications (LC), and infected necrosis (IN), and outcome in patients with AP. Flow cytometry was used to measure the percentage of peripheral blood mHLA-DR at different time points in 82 patients with AP enrolled during the period of 2012-2018 admitted to University Hospital Stara Zagora, Bulgaria. The percentages of peripheral blood mHLA-DR in AP patients were significantly associated with severity, development of LC, OF, IN (measured at admission, on the 48th hour and on the 5th day) and with outcome (measured on the 5th day) of AP. The value of peripheral blood mHLA-DR may be used as a biological marker in the diagnosis and assessment of severity, development of OF, LC, IN and to predict outcome in AP.

Acid suppression therapy, gastrointestinal bleeding and infection in acute pancreatitis - An international cohort study.

BACKGROUND: Acid suppressing drugs (ASD) are generally used in acute pancreatitis (AP); however, large cohorts are not available to understand their efficiency and safety. Therefore, our aims were to evaluate the association between the administration of ASDs, the outcome of AP, the frequency of gastrointestinal (GI) bleeding and GI infection in patients with AP. METHODS: We initiated an international survey and performed retrospective data analysis on AP patients hospitalized between January 2013 and December 2018. RESULTS: Data of 17,422 adult patients with AP were collected from 59 centers of 23 countries. We found that 23.3% of patients received ASDs before and 86.6% during the course of AP. ASDs were prescribed to 57.6% of patients at discharge. ASD administration was associated with more severe AP and higher mortality. GI bleeding was reported in 4.7% of patients, and it was associated with pancreatitis severity, mortality and ASD therapy. Stool culture test was performed in 6.3% of the patients with 28.4% positive results. Clostridium difficile was the cause of GI infection in 60.5% of cases. Among the patients with GI infections, 28.9% received ASDs, whereas 24.1% were without any acid suppression treatment. GI infection was associated with more severe pancreatitis and higher mortality. CONCLUSIONS: Although ASD therapy is widely used, it is unlikely to have beneficial effects either on the outcome of AP or on the prevention of GI bleeding during AP. Therefore, ASD therapy should be substantially decreased in the therapeutic management of AP.

A combination of C-reactive protein and quick sequential organ failure assessment (qSOFA) score has better prognostic accuracy than qSOFA alone in patients with complicated intra-abdominal infections.

INTRODUCTION: Complicated intra-abdominal infections (cIAIs) remain a serious challenge because of their unacceptably high mortality rates. Among different prognostic scoring systems quick-sequential organ failure assessment (qSOFA) score is the most recent. However, as mortality predictor in surgical patients, qSOFA showed lack of sensitivity. The aim of this study was to find prognostic superiority of our new qSOFA-CRP score in patients with cIAIs. MATERIALS AND METHODS: We retrospectively analyzed 78 patients presented to ED and admitted to Department of Surgical Diseases between January 2017 and October 2018 with diagnosis cIAIs. CRP levels, qSOFA score and systemic inflammatory response syndrome (SIRS) were established at admission. We analyzed area under receiver operating characteristics (AUROC) curves of SIRS, qSOFA and qSOFA-CRP and performed a comparison to explore their prognostic values. RESULTS: The identified in-hospital mortality was 25.6%. qSOFA-CRP score showed the best prognostic performance compared to qSOFA alone (AUROC = 0.818 vs. 0.746, p = .0219) and SIRS (AUROC = 0.818 vs. 0.579, p = .0009). The new qSOFA-CRP score ≥2 points showed excellent specificity (91.4%) and the highest sensitivity in comparison to qSOFA ≥2 and SIRS ≥2 (60% vs. 35% vs. 40%) for mortality prediction. CONCLUSIONS: qSOFA-CRP score showed better prognostic value than quick-SOFA alone in patients with cIAIs.

Poor Outcome Could Be Predicted by Lower Monocyte Human Leukocyte Antigen-DR Expression in Patients with Complicated Intra-Abdominal Infections: A Review.

Complicated intra-abdominal infections (cIAIs) are still associated with high morbidity and mortality levels. Early prognostic evaluation is a great challenge, and a serious amount of resources have been used to find the perfect mortality predictor. Monocyte human leukocyte antigen-DR (mHLA-DR) expression has been studied as a biomarker in patients with sepsis and other infections. Our aim was to evaluate the potential prognostic performance of mHLA-DR in patients with cIAIs. Methods: We performed an electronic search of Google Scholar and PubMed databases for articles published before January 2019. The search terms were "HLA-DR," "monocyte HLA-DR," "intra-abdominal infections," "sepsis," "outcome," and "mortality." Results: A total of 12 studies with 761 patients met our inclusion criteria. In 10 studies, poor outcome was predicted by lower mHLA-DR expression, and two studies showed no prognostic value. Conclusion: This review found association between lower mHLA-DR expression and mortality. We concluded that mHLA-DR could be a reliable and meaningful predictor of poor outcome in patients with cIAIs. Nevertheless, more large prospective studies with surgical patients exclusively are needed before using this biomarker in a clinical setting.

Neutrophil CD64 - A potential biomarker in patients with complicated intra-abdominal infections? - A literature review.

Complicated intra-abdominal infections (cIaIs) respresent a serious cause of morbidity and mortality. Early diagnosis and well-timed treatment can improve patients' outcome, whereas the delay in management often result in rapid progression to circulatory collapse, multiple organ failure, and death. Neutrophil CD64 antigen expression has been studied for several years as infectious and sepsis biomarker and has several characteristics that make it good for clinical employment. It has been suggested to be predictive of positive bacterial cultures and a useful test for management of sepsis and other significant bacterial infections. Our review concluded that the neutrophil CD64 expression could be a promising and meaningful biomarker in patients with cIaIs. It shows good potential for evaluating the severity of the disease and could give information about the outcome. However, more large studies should be performed before using it in clinical practice.

Increased Circulating CD4+CD25+CD127low/neg Regulatory T-cells as a Prognostic Biomarker in Acute Pancreatitis.

OBJECTIVE: Early detection of severe forms with unfavorable outcome is the cornerstone that could provide reduction of morbidity and mortality in acute pancreatitis (AP). METHODS: The percentage of circulating CD4CD25CD127 regulatory T-cells (Tregs) was determined at admission, on the 48th hour, and on the fifth day in 72 patients with AP. We divided patients in 2 groups-Sev1, which includes 19 patients (26.4%) with moderate AP and 39 patients (54.2%) with mild disease, and Sev2, which includes 14 patients (19.4%) with severe AP. Seven patients (9.7%) developed septic complications. The mortality in our group was 9.7%. RESULTS: The patients in Sev2 had higher percentage of Tregs at admission and on the fifth day compared with patients in Sev1 (P = 0.007 and P = 0.033, respectively). There was no significant difference in percentage of Tregs at admission, on the 48th hour, and on the fifth day in patients who developed and did not develop infected necrosis (P = 0.50, P = 0.72, and P = 0.92, respectively). Patients with poor outcome had elevated percentage of Tregs on the fifth day (P = 0.045). CONCLUSIONS: The percentage of circulating Tregs may be implicated in the development of early immune suppression in AP. Elevated percentage of circulating Tregs at admission in AP is an independent prognostic biomarker for severe disease.

Pathophysiological mechanisms of acute pancreatitis define inflammatory markers of clinical prognosis.

Development of acute pancreatitis illustrates the need to understand the basic mechanisms of disease progression to drive the exploration of therapeutic options. Cytokines play a major role in the pathogenesis of acute pancreatitis as underlying systemic inflammatory response, tissue damage, and organ dysfunction. However, little is known about circulating concentrations of these inflammatory markers and their real impact on clinical practice. Experimental studies have suggested that the prognosis for acute pancreatitis depends on the degree of pancreatic necrosis and the intensity of multisystem organ failure generated by the systemic inflammatory response. This suggests an intricate balance between localized tissue damage with proinflammatory cytokine production and a systemic anti-inflammatory response that restricts the inappropriate movement of proinflammatory agents into the circulation. Implication of such mediators suggests that interruption or blunting of an inappropriate immune response has the potential to improve outcome. A detailed understanding of pathophysiological processes and immunological aspects in patients with acute pancreatitis is the basis for the development of therapeutic strategies that will provide significant reductions in morbidity and mortality.

Insight into small RNA abundance and expression in high- and low-temperature stress response using deep sequencing in Arabidopsis.

Small RNA profiling and assessing its dependence on changing environmental factors have expanded our understanding of the transcriptional and post-transcriptional regulation of plant stress responses. Insufficient data have been documented earlier to depict the profiling of small RNA classes in temperature-associated stress which has a wide implication for climate change biology. In the present study, we report a comparative assessment of the genome-wide profiling of small RNAs in Arabidopsis thaliana using two conditional responses, induced by high- and low-temperature. Genome-wide profiling of small RNAs revealed an abundance of 21 nt small RNAs at low temperature, while high temperature showed an abundance of 21 nt and 24 nt small RNAs. The two temperature treatments altered the expression of a specific subset of mature miRNAs and displayed differential expression of a number of miRNA isoforms (isomiRs). Comparative analysis demonstrated that a large number of protein-coding genes can give rise to differentially expressed small RNAs following temperature shifts. Low temperature caused accumulation of small RNAs, corresponding to the sense strand of a number of cold-responsive genes. In contrast, high temperature stimulated the production of small RNAs of both polarities from genes encoding functionally diverse proteins.

Small RNA analysis of Potato spindle tuber viroid infected Phelipanche ramosa.

Plants defend themselves against virus/viroid infection by induction of a mechanism of viral RNA degradation or translation inhibition. This is achieved by the production of small RNAs referred to as small interfering RNAs and microRNA, the key molecules in establishment of RNA directed silencing. Potato Spindle Tuber Viroid (PSTVd) was the first viroid species to be identified as naturally infecting potato, and it was found to infect many other crop species, wild and ornamental plants. Recently the experimental host range of PSTVd was extended with the root non-photosynthetic parasitic weed--Phelipanche ramosa (L) Pomel. Here we examined the small RNA population in P. ramosa infected with PSTVd and we observed the presence of PSTVd derived small RNAs. The hotspot regions for production of those PSTVd specific small RNAs were defined by their mapping on the viroid genome sequence. Further, we evaluated the expression levels of selected conserved microRNA families in the viroid infected P. ramosa. Upon infection, two members of miRNA395 family were significantly accumulated, while several members of miRNA390, miRNA396, miRNA319, miRNA166, miRNA167 and miRNA159 were strongly down-regulated. All these findings imply the involvement of various small RNA classes in the P. ramosa response to PSTVd infection.

Epithelial cells expressing cytokeratins-19 and bone marrow micrometastases in patients with breast cancer at the time of primary surgery: clinical outcome during long-term follow-up.

PURPOSE: To evaluate the detection of epithelial cells in bone marrow of breast cancer patients as an indicator of metastatic disease. PATIENTS AND METHODS: Between 2001 and 2005, bone marrow biopsies were taken from 79 breast cancer patients during primary surgery. Specimens were stained immunocytochemically for epithelial cells expressing cytokeratins or epithelial membrane antigen. The long-term outcomes of these patients were analyzed. RESULTS: In 51 CK-positive results of 79 patients, epithelial cells were found in the bone marrow (BM) biopsies. These patients were designated CK(+). The rate of tumor recurrence or cancer-related death was significantly higher in CK(+) patients than in CK-negative patients. Multivariate analysis using the Cox regression model revealed BM status as a prognostic parameter independent of axillary lymph node status. CONCLUSION: Disseminated epithelial cells in BM are associated with poor clinical outcome in breast cancer patients. However, the presence of these cells is not a sufficient parameter, suggesting that epithelial cells in the BM of breast cancer patients at the time of surgery have limited metastatic potential. The role of these cells needs to be further evaluated.

isomiRex: web-based identification of microRNAs, isomiR variations and differential expression using next-generation sequencing datasets.

We present an open-access web platform isomiRex, to identify isomiRs and on the fly graphical visualization of the differentially expressed miRNAs in control as well as treated library. The open-access web-platform is not restricted only to NGS sequence dataset from animals and potentially analyzes a wider dataset for plants, animals and viral NGS dataset supporting miRBase (version 19 supporting 193 species). The platform can handle the bloated amount of the read counts and reports the annotated microRNAs from plant, animal and viral NGS datasets. isomiRex also provides an estimation of the the isomiRs, of miRNAs with higher copy number relative to their mature reference sequences indexed in miRBase (version 19 supporting 193 species). Visually enhanced graphs potentially display differentially expressed isomiRs, which will help the user to demonstrate and correlate the abundance of the isomiR as a signature event to the specific condition. An additional module for estimating the differential expression has been implemented allowing the users to postulate the differential expression across the user input samples. The developed web-platform can be accessed at http://bioinfo1.uni-plovdiv.bg/isomiRex/.

Implementation of a de novo genome-wide computational approach for updating Brachypodium miRNAs.

Plant microRNAs (miRNAs) are single-stranded 20-22 nt small RNAs (sRNA) that are produced from their own genes. We have developed a de novo genome-wide approach for the computational identification of novel plant miRNAs based on the integration of the complete genome sequence with sRNA libraries. It comprises three modules - the clustering module identifies genomic regions that have two closely-located unidirectional sRNA clusters, the mirplan module explores the secondary structure of the genomic regions, and the duplex module predicts miRNA/miRNA* duplexes. We applied our approach to the Brachypodium genome and publicly available sRNA libraries and predicted 102 miRNAs. Our results extend the list of known miRNAs with 58 novel miRNAs and define the genomic loci of all predicted miRNAs. Because this approach considers specific features of plant miRNAs, it can be employed for the analysis of the genome and sRNA libraries generated for plant species to achieve systematic miRNA discovery.